GtRNAdb

tRNAscan-SE Analysis of Gallus gallus (galGal3 May 2006)

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tRNA Gene Summary

tRNA-derived SINEs are found in a number of eukaryotes especially mammalian genomes. After manual inspection and analysis, we apply the following filter to this genome for eliminating these tRNA-derived elements from true tRNAs. If the tRNA candidates have hits in both tRNAscan and Eufind first-pass scanners, we use a combination of at least 20 bits COVE score, 10 bits HMM score, and 5 bits 2' structure score to define a true tRNA. If the tRNA candidates only have hits in one of the first-pass scanners, the threshold of a true tRNA will be 55 bits COVE score.





tRNAs Decoding Standard 20 AA241
Selenocysteine tRNAs (TCA)1
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
0
Predicted pseudogenes0
Total tRNAs242


Intron Summary

tRNAs with introns
12
Arg
TCT
2
Leu
CAA
2
Ile
TAT
2
Tyr
GTA
6


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
19
GGC
1
CGC
2
TGC
7
29
GlyACC
 
GCC
5
CCC
4
TCC
8
17
ProAGG
6
GGG
 
CGG
2
TGG
3
11
ThrAGT
4
GGT
 
CGT
2
TGT
4
10
ValAAC
7
GAC
1
CAC
5
TAC
3
16

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
8
GGA
 
CGA
2
TGA
4
ACT
 
GCT
6
 
 
 
 
20
ArgACG
6
GCG
 
CCG
2
TCG
2
 
 
 
 
CCT
3
TCT
3
16
LeuAAG
3
GAG
 
CAG
6
TAG
1
 
 
 
 
CAA
2
TAA
2
14

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
1
GAA
9
 
 
 
 
10
AsnATT
 
GTT
9
 
 
 
 
9
Lys 
 
 
 
CTT
6
TTT
3
9
AspATC
 
GTC
8
 
 
 
 
8
Glu 
 
 
 
CTC
7
TTC
7
14
HisATG
1
GTG
7
 
 
 
 
8
Gln 
 
 
 
CTG
3
TTG
3
6

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
7
GAT
 
 
 
TAT
2
9
Met 
 
 
 
CAT
13
 
 
13
TyrATA
 
GTA
6
 
 
 
 
6
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
10
 
 
 
 
10
Trp 
 
 
 
CCA
6
 
 
6
SelCys 
 
 
 
 
 
TCA
1
1

The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.